No alignment inside the BAM file

[TaiwoUoB]

Dear All, I am using STAR aligner to map the Paired RNA seq reads to genome data using the below scripts: ./STAR --runMode alignReads --runThreadN 16 --genomeDir /home/taiwo/star/STAR-2.5.3a/bin/Linux_x86_64 --outFileNamePrefix star_alignment --readFilesCommand zcat --readFilesIn SRR8278105.fastq --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif. It ran for few minutes and successfully finished. When i checked, there is no alignment in the bam file. Please can i do and missing out. Your suggestions would be appreciated.

[alexdobin]

Hi @TaiwoUoB

since your files are unzipped, please try to remove --readFilesCommand zcat option. This option should only be used for zipped (.gz) files.

Cheers Alex

[TaiwoUoB]

Hello Alex, Many thanks, i will try that now and let you know.

Taiwo

[TaiwoUoB]

Hello Alex, I got a message when I ran it without the --readFilesCommand zcat option. See the error message below and advise, please. (base) taiwo@zetaadmin:/home/taiwo/star/STAR-2.5.3a/bin/Linux_x86_64$ ./STAR --runMode alignReads --runThreadN 16 --genomeDir /home/taiwo/star/STAR-2.5.3a/bin/Linux_x86_64 --outFileNamePrefix star_alignment --readFilesIn SRR8278105.fastq --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif Jan 20 10:51:39 ..... started STAR run Jan 20 10:51:39 ..... loading genome Jan 20 10:51:40 ..... started mapping

ReadAlignChunk_processChunks.cpp:115:processChunks EXITING because of FATAL ERROR in input reads: unknown file format: the read ID should start with @ or >

Jan 20 10:51:41 ...... FATAL ERROR, exiting (base) taiwo@zetaadmin:/home/taiwo/star/STAR-2.5.3a/bin/Linux_x86_64$

[alexdobin]

Hi @TaiwoUoB

how did you download this file from SRA? Did you use the --split-files option in fastq-dump? Could you post ~20 first lines of the fastq file?

Cheers Alex